test15

workflow.wdl

 			disk_size=disk_size
 		}
 	} 
-	else {
-		# Fastq is null, check if starts with vcf
-		if (!defined(vcf_D5) && !defined(vcf_D6) && !defined(vcf_F7) && !defined(vcf_M8) ) {
-			call rename_vcf.rename_vcf as rename_vcf{
-				input:
-				vcf_D5=vcf_D5,
-				vcf_D6=vcf_D6,
-				vcf_F7=vcf_F7,
-				vcf_M8=vcf_M8,
-				project=project,
-				docker=DIYdocker,
-				cluster_config=SMALLcluster_config,
-				disk_size=disk_size
-			}
-			call filter_vcf.filter_vcf as filter_vcf_D5_vcf {
-				input:
-				vcf=rename_vcf.vcf_D5_renamed,
-				docker=BEDTOOLSdocker,
-				cluster_config=SMALLcluster_config,
-				disk_size=disk_size			
-			}
-
-			call benchmark.benchmark as benchmark_D5_vcf {
-				input:
-				filtered_vcf=filter_vcf_D5_vcf.filtered_vcf,
-				benchmarking_dir=benchmarking_dir,
-				ref_dir=ref_dir,
-				fasta=fasta,
-				docker=BENCHMARKdocker,
-				cluster_config=BIGcluster_config,
-				disk_size=disk_size
-			}
-
-			call filter_vcf.filter_vcf as filter_vcf_D6_vcf {
-				input:
-				vcf=rename_vcf.vcf_D6_renamed,
-				docker=BEDTOOLSdocker,
-				cluster_config=SMALLcluster_config,
-				disk_size=disk_size			
-			}
-
-			call benchmark.benchmark as benchmark_D6_vcf {
-				input:
-				filtered_vcf=filter_vcf_D6_vcf.filtered_vcf,
-				benchmarking_dir=benchmarking_dir,
-				ref_dir=ref_dir,
-				fasta=fasta,
-				docker=BENCHMARKdocker,
-				cluster_config=BIGcluster_config,
-				disk_size=disk_size
-			}
-
-			call filter_vcf.filter_vcf as filter_vcf_F7_vcf {
-				input:
-				vcf=rename_vcf.vcf_F7_renamed,
-				docker=BEDTOOLSdocker,
-				cluster_config=SMALLcluster_config,
-				disk_size=disk_size			
-			}
-
-			call benchmark.benchmark as benchmark_F7_vcf {
-				input:
-				filtered_vcf=filter_vcf_F7_vcf.filtered_vcf,
-				benchmarking_dir=benchmarking_dir,
-				ref_dir=ref_dir,
-				fasta=fasta,
-				docker=BENCHMARKdocker,
-				cluster_config=BIGcluster_config,
-				disk_size=disk_size
-			}
-
-			call filter_vcf.filter_vcf as filter_vcf_M8_vcf {
-				input:
-				vcf=rename_vcf.vcf_M8_renamed,
-				docker=BEDTOOLSdocker,
-				cluster_config=SMALLcluster_config,
-				disk_size=disk_size			
-			}
-
-			call benchmark.benchmark as benchmark_M8_vcf {
-				input:
-				filtered_vcf=filter_vcf_M8_vcf.filtered_vcf,
-				benchmarking_dir=benchmarking_dir,
-				ref_dir=ref_dir,
-				fasta=fasta,
-				docker=BENCHMARKdocker,
-				cluster_config=BIGcluster_config,
-				disk_size=disk_size
-			}
-
-			Array[File] benchmark_summary_hap = [benchmark_D5_vcf.summary, benchmark_D6_vcf.summary, benchmark_F7_vcf.summary, benchmark_M8_vcf.summary]
-
-			call multiqc_hap.multiqc_hap as multiqc_hap {
-				input:
-				summary=benchmark_summary_hap,
-				docker=MULTIQCdocker,
-				cluster_config=SMALLcluster_config,
-				disk_size=disk_size
-			}
-
-			call extract_tables_vcf.extract_tables_vcf as extract_tables_vcf {
-				input:
-				hap=multiqc_hap.hap,
-				project=project,
-				docker=DIYdocker,
-				cluster_config=SMALLcluster_config,
-				disk_size=disk_size
-			}
-
-			call merge_family.merge_family as merge_family_vcf {
-				input:
-				D5_vcf=benchmark_D5_vcf.rtg_vcf,
-				D6_vcf=benchmark_D6_vcf.rtg_vcf,
-				F7_vcf=benchmark_F7_vcf.rtg_vcf,
-				M8_vcf=benchmark_M8_vcf.rtg_vcf,
-				D5_vcf_tbi=benchmark_D5_vcf.rtg_vcf_index,
-				D6_vcf_tbi=benchmark_D6_vcf.rtg_vcf_index,
-				F7_vcf_tbi=benchmark_F7_vcf.rtg_vcf_index,
-				M8_vcf_tbi=benchmark_M8_vcf.rtg_vcf_index,
-				project=project,
-				docker=BENCHMARKdocker,
-				cluster_config=SMALLcluster_config,
-				disk_size=disk_size,
-			}
-
-			call mendelian.mendelian as mendelian_vcf {
-				input:
-				family_vcf=merge_family_vcf.family_vcf,
-				ref_dir=ref_dir,
-				fasta=fasta,
-				docker=MENDELIANdocker,
-				cluster_config=BIGcluster_config,
-				disk_size=disk_size		
-			}
-
-			call merge_mendelian.merge_mendelian as merge_mendelian_vcf {
-				input:
-				D5_trio_vcf=mendelian_vcf.D5_trio_vcf,
-				D6_trio_vcf=mendelian_vcf.D6_trio_vcf,
-				family_vcf=merge_family_vcf.family_vcf,
-				docker=DIYdocker,
-				cluster_config=SMALLcluster_config,
-				disk_size=disk_size
-			}
+	
+	# Fastq is null, check if starts with vcf
+	if (!defined(vcf_D5) && !defined(vcf_D6) && !defined(vcf_F7) && !defined(vcf_M8) ) {
+		call rename_vcf.rename_vcf as rename_vcf{
+			input:
+			vcf_D5=vcf_D5,
+			vcf_D6=vcf_D6,
+			vcf_F7=vcf_F7,
+			vcf_M8=vcf_M8,
+			project=project,
+			docker=DIYdocker,
+			cluster_config=SMALLcluster_config,
+			disk_size=disk_size
+		}
+		call filter_vcf.filter_vcf as filter_vcf_D5_vcf {
+			input:
+			vcf=rename_vcf.vcf_D5_renamed,
+			docker=BEDTOOLSdocker,
+			cluster_config=SMALLcluster_config,
+			disk_size=disk_size			
+		}
+
+		call benchmark.benchmark as benchmark_D5_vcf {
+			input:
+			filtered_vcf=filter_vcf_D5_vcf.filtered_vcf,
+			benchmarking_dir=benchmarking_dir,
+			ref_dir=ref_dir,
+			fasta=fasta,
+			docker=BENCHMARKdocker,
+			cluster_config=BIGcluster_config,
+			disk_size=disk_size
+		}
+
+		call filter_vcf.filter_vcf as filter_vcf_D6_vcf {
+			input:
+			vcf=rename_vcf.vcf_D6_renamed,
+			docker=BEDTOOLSdocker,
+			cluster_config=SMALLcluster_config,
+			disk_size=disk_size			
+		}
+
+		call benchmark.benchmark as benchmark_D6_vcf {
+			input:
+			filtered_vcf=filter_vcf_D6_vcf.filtered_vcf,
+			benchmarking_dir=benchmarking_dir,
+			ref_dir=ref_dir,
+			fasta=fasta,
+			docker=BENCHMARKdocker,
+			cluster_config=BIGcluster_config,
+			disk_size=disk_size
+		}
+
+		call filter_vcf.filter_vcf as filter_vcf_F7_vcf {
+			input:
+			vcf=rename_vcf.vcf_F7_renamed,
+			docker=BEDTOOLSdocker,
+			cluster_config=SMALLcluster_config,
+			disk_size=disk_size			
+		}
+
+		call benchmark.benchmark as benchmark_F7_vcf {
+			input:
+			filtered_vcf=filter_vcf_F7_vcf.filtered_vcf,
+			benchmarking_dir=benchmarking_dir,
+			ref_dir=ref_dir,
+			fasta=fasta,
+			docker=BENCHMARKdocker,
+			cluster_config=BIGcluster_config,
+			disk_size=disk_size
+		}
+
+		call filter_vcf.filter_vcf as filter_vcf_M8_vcf {
+			input:
+			vcf=rename_vcf.vcf_M8_renamed,
+			docker=BEDTOOLSdocker,
+			cluster_config=SMALLcluster_config,
+			disk_size=disk_size			
+		}
+
+		call benchmark.benchmark as benchmark_M8_vcf {
+			input:
+			filtered_vcf=filter_vcf_M8_vcf.filtered_vcf,
+			benchmarking_dir=benchmarking_dir,
+			ref_dir=ref_dir,
+			fasta=fasta,
+			docker=BENCHMARKdocker,
+			cluster_config=BIGcluster_config,
+			disk_size=disk_size
+		}
+
+		Array[File] benchmark_summary_hap = [benchmark_D5_vcf.summary, benchmark_D6_vcf.summary, benchmark_F7_vcf.summary, benchmark_M8_vcf.summary]
+
+		call multiqc_hap.multiqc_hap as multiqc_hap {
+			input:
+			summary=benchmark_summary_hap,
+			docker=MULTIQCdocker,
+			cluster_config=SMALLcluster_config,
+			disk_size=disk_size
+		}
+
+		call extract_tables_vcf.extract_tables_vcf as extract_tables_vcf {
+			input:
+			hap=multiqc_hap.hap,
+			project=project,
+			docker=DIYdocker,
+			cluster_config=SMALLcluster_config,
+			disk_size=disk_size
+		}
+
+		call merge_family.merge_family as merge_family_vcf {
+			input:
+			D5_vcf=benchmark_D5_vcf.rtg_vcf,
+			D6_vcf=benchmark_D6_vcf.rtg_vcf,
+			F7_vcf=benchmark_F7_vcf.rtg_vcf,
+			M8_vcf=benchmark_M8_vcf.rtg_vcf,
+			D5_vcf_tbi=benchmark_D5_vcf.rtg_vcf_index,
+			D6_vcf_tbi=benchmark_D6_vcf.rtg_vcf_index,
+			F7_vcf_tbi=benchmark_F7_vcf.rtg_vcf_index,
+			M8_vcf_tbi=benchmark_M8_vcf.rtg_vcf_index,
+			project=project,
+			docker=BENCHMARKdocker,
+			cluster_config=SMALLcluster_config,
+			disk_size=disk_size,
+		}
+
+		call mendelian.mendelian as mendelian_vcf {
+			input:
+			family_vcf=merge_family_vcf.family_vcf,
+			ref_dir=ref_dir,
+			fasta=fasta,
+			docker=MENDELIANdocker,
+			cluster_config=BIGcluster_config,
+			disk_size=disk_size		
+		}
+
+		call merge_mendelian.merge_mendelian as merge_mendelian_vcf {
+			input:
+			D5_trio_vcf=mendelian_vcf.D5_trio_vcf,
+			D6_trio_vcf=mendelian_vcf.D6_trio_vcf,
+			family_vcf=merge_family_vcf.family_vcf,
+			docker=DIYdocker,
+			cluster_config=SMALLcluster_config,
+			disk_size=disk_size
 		}
 	}
+	
 }